[gmx-users] pbc whole

[Tsjerk Wassenaar]

Hi Carla,

Justin's recipe should've worked. As he suggested, maybe the ligand is
not with the protein. You can check by multiplying your system with
genconf:

genconf -f in.pdb -o out.pdb -nbox 2 2 2

If the ligand is with the protein, one copy will be located in one of
the copies of the protein.

g_rmsf does write the average structure, if requested. Use the option -ox

Cheers,

Tsjerk

On Wed, Feb 17, 2010 at 10:08 AM, Carla Jamous <carlajamous at gmail.com> wrote:
> Hi Justin,
> I'm still trying to figure out what happened with my ligand.
> Meanwhile, I have another question: I can't figure out how to calculate an
> average structure in gromacs.
> And does g_rmsf calculate the average structure automatically?
>
> Thanks again
> Carla
>
> On Tue, Feb 16, 2010 at 5:44 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> Carla Jamous wrote:
>>>
>>> Hi Justin,
>>> Thank you for your answer but I'm still not getting my ligand to stay in
>>> the box.
>>>
>>> I tried the following(after taking a look at the mailing list archive):
>>>
>>> trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol
>>> (centering on "Protein")
>>> trjconv -s d.tpr -f c.xtc -o f.xtc -fit rot+trans
>>>
>>> So please do you have another advise to give me?
>>>
>>
>> If that's not working, then I wonder if your ligand is still actually
>> bound to your protein :)  The above sequence always works for me, as long as
>> there actually is a complex.  You can also try -pbc cluster, but I know that
>> algorithm can hang.
>>
>> -Justin
>>
>>> Thanks
>>> Carla
>>>
>>> On Mon, Feb 15, 2010 at 4:32 PM, Justin A. Lemkul <jalemkul at vt.edu
>>> <mailto:jalemkul at vt.edu>> wrote:
>>>
>>>
>>>
>>>    Carla Jamous wrote:
>>>
>>>        Hi everyone,
>>>        I'm using this command to extract my protein and my ligand from
>>>        the trajectory.
>>>
>>>        trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc
>>>        whole -n prot_wat.ndx -o prot_ligand_60ns.xtc < grps >& outtrj
>>>
>>>        Before, I had a problem with residues of my protein showing at
>>>        the other end of the box, when I display my .xtc with VMD.
>>>        the "-pbc whole" fixed it.
>>>
>>>        However, now I have another issue: my ligand is at the other end
>>>        of the box. So please can anyone tell me what can I do to fix
>>>        that and get a reasonable RMSD value?
>>>
>>>
>>>    You may need several more iterations of trjconv (one rarely does the
>>>    trick), employing -pbc nojump, -pbc cluster, and/or -center.  For
>>>    protein-ligand complexes, I have often found that the combination of:
>>>
>>>    trjconv -pbc mol -ur compact -center
>>>
>>>    (centering on "Protein")
>>>
>>>    does the trick.  And it makes molecules whole, as well :)  I think
>>>    there are also some breakdowns (documented somewhere in the list
>>>    archive) when applying -fit and -pbc in the same step.  I believe it
>>>    is recommended to fix PBC first, then applying any sort of fitting
>>>    in a separate, subsequent step.
>>>
>>>    -Justin
>>>
>>>        Thank you
>>>        Carla
>>>
>>>
>>>    --    ========================================
>>>
>>>    Justin A. Lemkul
>>>    Ph.D. Candidate
>>>    ICTAS Doctoral Scholar
>>>    MILES-IGERT Trainee
>>>    Department of Biochemistry
>>>    Virginia Tech
>>>    Blacksburg, VA
>>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>>    ========================================
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>>>
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist